sorry, I don't think it completed as unzip can't find the end of directory mark in the file. Try our filedrop instead:
https://gate.nmr.mgh.harvard.edu/filedrop2/
cheers Bruce
On Mon, 7 Oct 2013, Marcos Martins da Silva wrote:
Hi, Bruce I proceeded as explained at http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange . Using ftp method, it started at good rate but after I transferred about 3/4 of the file the transfer rate decreased to some bytes (not Kbytes) per second. Tried using curl -T and it seemed to complete after about 50 min but I got this message on terminal: DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head> <title>405 Method Not Allowed</title> </head><body> <h1>Method Not Allowed</h1> <p>The requested method PUT is not allowed for the URL /transfer/incoming.</p> <hr> <address>Apache/2.2.15 (CentOS) Server at surfer.nmr.mgh.harvard.edu Port 80</address> </body></html>
So I am not sure you received the file. You should find a suj46.zip corresponding to the complete folder from my subject 46. You will find the usual structure created by recon-all. At mri folder you will find all the usual volumes, the posterior* files generated by hippo-subfield processing and the files I created on my analysis. Please, could you check if you really received the file? If not, I will try again using plain ftp. Thank you again for your help. Marcos. Em Seg, 2013-10-07 às 09:21 -0400, Bruce Fischl escreveu:
hmmm, I guess you should upload the subject so that we can track it down On Mon, 7 Oct 2013, Marcos Martins da Silva wrote:
Hi, Bruce. Thank you for your fast answer. I used a script and It took less than 15 min to process all files from all
subjects, except
the 3 files (surfaces) mris_smooth seems to enter a loop. When I tried to
smooth
surfLeftHippobody I waited for more than 4 hours. Comparing to the total t
ime I needed to
process all files I concluded something was wrong and esed control + C to
interrupt the
process. I tested on 2 machines (mine is running CentOS 6 and the second i
s a Mac, both using
Freesurfer 5.3) and got the same result. Including they seem to stop at th
e same point. Do you
think it could need more time to finnish processing? Alternatively, as I can use mris_smooth to process the whole left hippocam
pus (the problem
only appears when processing the body segment), I guess I could get a simi
lar and perhaps
better result if I could make a label from each of the binary masks of the
3 segments (head,
body, tail), merge them in an annot file and finally load the whole surfac
e and the annot file
so I get the 3 segments discriminated by color. I found on Freesurfer Wiki
how to merge the
labels into an annot file but not how to make the labels from the binary m
asks.
Thank you for your attention.
2013/10/4 Bruce Fischl fischl@nmr.mgh.harvard.edu how long have you waited?
On Fri, 4 Oct 2013, Marcos Martins da Silva wrote:
Hi, Freesurfers I am getting some interesting hippocampal surfaces with the fo
llowing
steps: 1- recon-all -all -hippo-subfields 2- mri-concat (only CA1, CA23, CA4DG and the tail complement v
olumes)
3- a custom OCTAVE script to segment the concatenated volume f
rom step
2 into Head, Body and Tail 4- mri_binarize Head, Body and Tail volumes from step 3 5- mri_tessellate the binary masks from step 4 6- mri_smooth the surfaces from step 5
Using freeview I got a screenshot showing both hippocampi segm
ented
(hipposurf3d.png is attached). This approach worked well for 16 subjects up to step 5. Step 6
was
completed as well in 13 out 16 subjects.
The only problem was during left hippocampal body smoothing in
3
subjects (all the other surfaces from all 16 subjects in were smoothed
with no
problem). For these 3 surfaces, mris_smooth simply freezes, wi
th no
error message. I must press control + C to quit the program. During
the
freezing I noticed high CPU use. It follows the exactly command I used and the screen output.
mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoBody lh.surfHipp
oBody
using Gaussian curvature smoothing with norm 5.00 with 2 smoot
h steps
averaging curvature for 1 iterations smoothing for 1 iterations smoothing surface tessellation for 1 iterations... ------------------------------------------------------ ------------------------------------------------------ ------------------ pass 1 (num=2853) ------------------ ------------------------------------------------------ ------------------------------------------------------
If I supress the gaussian parameters and run just something li
ke:
mris_smooth -nw -a 1 -n 1 surfLeftHippoBody lh.surfHippoBody or even mris_smooth -nw surfLeftHippoBody lh.surfHippoBody
I got the smoothed surface with no errors but the final qualit
y is not
as good as when I use the gaussian parameters. I am attaching one of the problematic surface files so you can
check
it (surfLeftHippobody). Intersting if I use a surface with all le
ft
hippocampus (including head, problematic body and tail and) smoothing comp
letes
without error Thank you very much for any help. Marcos
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